Can Zhong 1,2, Jian Jin 2, Rongrong Zhou 3, Hao Liu 2, Jing Xie2, Dan Wan2, Shengen Xiao1*, and Shuihan Zhang 1,2*
1 Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, P. R. China,2 Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha 410013, P. R. China,3 Changchun University of Chinese Medicine, Changchun 130117, P. R. China.* Correspondence: 2395265030@qq.com (S. X.),zhangshuihan0220@126.com(S.Z.) Received: date; Accepted: date; Published: date
Abstract: Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of O. xuefengensis , in addition to comparing it against three other complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the O. sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs andrps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships betweenO. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis . Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.
Keywords: cordyceps, mitochondrial genome, phylogenetic analysis, introns
1. Introduction
Mitochondrial genomes are powerful tools that can be used in phylogenetic and evolutionary studies [1-4], owing to their small size, high copy numbers, conserved orthologous genes, rare instances of recombination, and high evolutionary rates [5]. The rapid development of new genome sequencing technologies in recent years has led to the production of more than 180 fungal mitogenomes. Fungal mitochondria range in length from approximately 11 kbp (Hanseniaspora uvarum ) to 272.2 kbp (Morchella importuna ), depending on the species, but usually contain 14 conserved genes [6]. In addition, mitogenome characteristics, including genome size, genome structure, gene content, gene arrangement, tRNA number, intron number, codon usage, and repeat content, can provide useful information to understand the origin, evolution, and systematics of eukaryotes [7-9].
”Cordyceps” comprises four genera including Cordyceps ,Ophiocordyceps , Metacordyceps , and Elaphocordyceps . The fungi have been used in traditional Chinese medicine, as dietary supplements, or as tonic edibles with broad pharmacological properties including antibacterial, antiviral, and antitumor activities, in addition to the ability to enhance human immunity [10, 11]. AlthoughCordyceps have considerable economic and medicinal significance, wild cordyceps resources are on the verge of exhaustion, leading to many investigators seeking alternatives. Among these,O. xuefengensis is a newly identified cordyceps resource that we previously discovered on Xuefeng mountain in the Hunan province of China [12]. The novel taxa has been widely used as an ethnopharmacological invigorant by the Yao group for a long time [13]. Further, we have successfully cultivated this cordyceps fungi and also characterized some of its chemical metabolites [14]. Cordyceps andOphiocordyceps are the two most widely used groups of cordyceps fungi. In particular, O. sinensis is popularly used to treat many diseases in China. Consequently, the cultivation, novel metabolite compounds, and pharmacology of cordyceps fungi have been extensively researched, although further molecular phylogenetic and species identification studies are critically needed.
In the present study, the complete mitogenome from O. xuefengensis was sequenced, assembled, and compared to three other complete cordyceps mitogenomes that were previously reported. This study thereby represents the first comparative analysis of the genomic structure, base composition, substitution and evolutionary rates among four cordyceps species, in addition to the comprehensive molecular phylogenetic analysis of cordyceps in the Hypocreales order. The present study aimed to expand our knowledge of the diversity of mitochondrial genomes and phylogenetic relationships of cordyceps.
2. Materials and Methods